{"id":"https://openalex.org/W2950620935","doi":"https://doi.org/10.18653/v1/w19-5032","title":"Embedding Biomedical Ontologies by Jointly Encoding Network Structure and Textual Node Descriptors","display_name":"Embedding Biomedical Ontologies by Jointly Encoding Network Structure and Textual Node Descriptors","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2950620935","doi":"https://doi.org/10.18653/v1/w19-5032","mag":"2950620935"},"language":"en","primary_location":{"id":"doi:10.18653/v1/w19-5032","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w19-5032","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 18th BioNLP Workshop and Shared Task","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.18653/v1/w19-5032","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028096821","display_name":"Sotiris Kotitsas","orcid":null},"institutions":[{"id":"https://openalex.org/I73142707","display_name":"Athens University of Economics and Business","ror":"https://ror.org/03s262162","country_code":"GR","type":"education","lineage":["https://openalex.org/I73142707"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Sotiris Kotitsas","raw_affiliation_strings":["Athens University of Economics and Business, Athens, Greece"],"affiliations":[{"raw_affiliation_string":"Athens University of Economics and Business, Athens, Greece","institution_ids":["https://openalex.org/I73142707"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001794274","display_name":"Dimitris Pappas","orcid":"https://orcid.org/0000-0001-5784-0658"},"institutions":[{"id":"https://openalex.org/I73142707","display_name":"Athens University of Economics and Business","ror":"https://ror.org/03s262162","country_code":"GR","type":"education","lineage":["https://openalex.org/I73142707"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Dimitris Pappas","raw_affiliation_strings":["Athens University of Economics and Business, Athens, Greece"],"affiliations":[{"raw_affiliation_string":"Athens University of Economics and Business, Athens, Greece","institution_ids":["https://openalex.org/I73142707"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069270736","display_name":"Ion Androutsopoulos","orcid":"https://orcid.org/0009-0000-2969-0509"},"institutions":[{"id":"https://openalex.org/I73142707","display_name":"Athens University of Economics and Business","ror":"https://ror.org/03s262162","country_code":"GR","type":"education","lineage":["https://openalex.org/I73142707"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Ion Androutsopoulos","raw_affiliation_strings":["Athens University of Economics and Business, Athens, Greece"],"affiliations":[{"raw_affiliation_string":"Athens University of Economics and Business, Athens, Greece","institution_ids":["https://openalex.org/I73142707"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022489655","display_name":"Ryan McDonald","orcid":null},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan McDonald","raw_affiliation_strings":["Google (United States), Mountain View, United States"],"affiliations":[{"raw_affiliation_string":"Google (United States), Mountain View, United States","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003714034","display_name":"Marianna Apidianaki","orcid":"https://orcid.org/0000-0002-8785-7722"},"institutions":[{"id":"https://openalex.org/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Marianna Apidianaki","raw_affiliation_strings":["D\u00e9l\u00e9gation Paris 7, Bagnolet, France"],"affiliations":[{"raw_affiliation_string":"D\u00e9l\u00e9gation Paris 7, Bagnolet, France","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I169173203"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5028096821"],"corresponding_institution_ids":["https://openalex.org/I73142707"],"apc_list":null,"apc_paid":null,"fwci":0.3425,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.59092681,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"298","last_page":"308"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.9958000183105469,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7458550930023193},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.6694874167442322},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6566399931907654},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.5571929216384888},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.5533572435379028},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5222930908203125},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5111199021339417},{"id":"https://openalex.org/keywords/network-structure","display_name":"Network structure","score":0.48381584882736206},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4444807171821594},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4199366867542267},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35156190395355225}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7458550930023193},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.6694874167442322},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6566399931907654},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.5571929216384888},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.5533572435379028},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5222930908203125},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5111199021339417},{"id":"https://openalex.org/C2988224531","wikidata":"https://www.wikidata.org/wiki/Q20830730","display_name":"Network structure","level":2,"score":0.48381584882736206},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4444807171821594},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4199366867542267},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35156190395355225},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.18653/v1/w19-5032","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w19-5032","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 18th BioNLP Workshop and Shared Task","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:1906.05939","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1906.05939","pdf_url":"https://arxiv.org/pdf/1906.05939","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"mag:2950620935","is_oa":true,"landing_page_url":"http://export.arxiv.org/pdf/1906.05939","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1906.05939","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1906.05939","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.18653/v1/w19-5032","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/w19-5032","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 18th BioNLP Workshop and Shared Task","raw_type":"proceedings-article"},"sustainable_development_goals":[{"score":0.6000000238418579,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1979104937","https://openalex.org/W1997585114","https://openalex.org/W2041428546","https://openalex.org/W2101234009","https://openalex.org/W2117130368","https://openalex.org/W2131774270","https://openalex.org/W2134418889","https://openalex.org/W2153579005","https://openalex.org/W2153959628","https://openalex.org/W2157331557","https://openalex.org/W2159583324","https://openalex.org/W2185246716","https://openalex.org/W2189149359","https://openalex.org/W2194775991","https://openalex.org/W2393319904","https://openalex.org/W2530041791","https://openalex.org/W2604314403","https://openalex.org/W2740934577","https://openalex.org/W2785951678","https://openalex.org/W2808987817","https://openalex.org/W2890881127","https://openalex.org/W2899771611","https://openalex.org/W2933100986","https://openalex.org/W2962756421","https://openalex.org/W2963157208","https://openalex.org/W2963626623","https://openalex.org/W2963918774","https://openalex.org/W2964121744","https://openalex.org/W2964126306","https://openalex.org/W2964198126","https://openalex.org/W2964308564","https://openalex.org/W3104097132","https://openalex.org/W3105705953"],"related_works":["https://openalex.org/W2969964888","https://openalex.org/W2798756592","https://openalex.org/W3163920200","https://openalex.org/W3033623365","https://openalex.org/W3039055350","https://openalex.org/W2942962046","https://openalex.org/W2997964288","https://openalex.org/W2796988304","https://openalex.org/W3012111473","https://openalex.org/W2951690208","https://openalex.org/W2808340618","https://openalex.org/W3130747874","https://openalex.org/W2940847211","https://openalex.org/W2889779965","https://openalex.org/W3007974554","https://openalex.org/W3184838450","https://openalex.org/W2966218129","https://openalex.org/W2998930655","https://openalex.org/W3135509807","https://openalex.org/W2798785997"],"abstract_inverted_index":{"Network":[0],"Embedding":[1],"(NE)":[2],"methods,":[3],"which":[4],"map":[5],"network":[6,16,27,53,65],"nodes":[7],"to":[8,43,67,100],"low-dimensional":[9],"feature":[10],"vectors,":[11],"have":[12],"wide":[13],"applications":[14],"in":[15,84],"analysis":[17],"and":[18],"bioinformatics.":[19],"Many":[20],"existing":[21],"NE":[22,60],"methods":[23],"rely":[24],"only":[25,50],"on":[26,81],"structure,":[28,66],"overlooking":[29],"other":[30],"information":[31,49],"associated":[32],"with":[33],"the":[34,39,45,93,96],"nodes,":[35],"e.g.,":[36],"text":[37],"describing":[38],"nodes.":[40],"Recent":[41],"attempts":[42],"combine":[44],"two":[46,85],"sources":[47],"of":[48,95],"consider":[51,69],"local":[52],"structure.":[54],"We":[55],"extend":[56],"NODE2VEC,":[57],"a":[58],"well-known":[59],"method":[61,78],"that":[62],"considers":[63],"broader":[64],"also":[68],"textual":[70],"node":[71],"descriptors":[72],"using":[73],"recurrent":[74],"neural":[75],"encoders.":[76],"Our":[77],"is":[79],"evaluated":[80],"link":[82],"prediction":[83],"networks":[86],"derived":[87],"from":[88],"UMLS.":[89],"Experimental":[90],"results":[91],"demonstrate":[92],"effectiveness":[94],"proposed":[97],"approach":[98],"compared":[99],"previous":[101],"work.":[102]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
